Biology subjects

Borsa, M.

Publications and source records attributed to Borsa, M..

12 recordsLinked to original sources

bioRxiv2026

Lack of Consensus for Manual Mouse Sleep Scoring Limits Implementation of Automatic Deep Learning Models

Scientists have for decades attempted to automate the manual sleep staging problem not only for human polysomnography data but also for rodent data. No model has, however, succeeded in fully replacing the manual procedure across clinics and laboratories. We hypothesize that this is due to the models limited ability to generalize to data from unseen laboratories. Our findings show that despite the high performance of four state-of-the-art models reported in initial publications, the published models struggle to generalize to other laboratories. We further show a significant improvement in model performance across labs by re-training them on a diverse dataset from five different sites. To assess the contribution of variability in manual scoring, ten experts from five laboratories all labelled the same nine mouse sleep recordings. The result revealed substantial scoring variability, particularly for rapid eye movement (REM) sleep, both within and between labs. In conclusion our study demonstrates that key challenges in the generalizability of state-of-the-art sleep scoring models are signal variability and label noise. Our study highlights the need for a standardized set of mouse sleep scoring guidelines to enable consistency and collaboration across the field. Until such a consensus is reached, we present four sufficiently robust models trained on diverse datasets that can serve as standardized tools across labs.

neuroscience↗

bioRxiv2026

Transient immune landscape remodelling shapes CD8 T-cell priming during infection

Immune responses to intracellular pathogens require the generation of a CD8 T-cell response comprised of clones with a broad range of T Cell Receptor (TCR) affinities for their cognate peptide. While high-affinity clones clear pathogens during initial infection, low-affinity T-cells are critical to protect against subsequent encounters with mutated pathogens. Low-affinity T-cells are recruited to an immune response despite known mechanisms that limit their expansion and priming. As such, the mechanism safeguarding the recruitment of low-affinity T-cell clones during infection remains unclear. Here, we show that at the start of an infection, the spatial immune architecture is transiently reorganised to initiate broad T-cell priming. In particular, Tregs become segregated from the initial priming site, resulting in a spatio-temporal window during which pathogen-specific T-cell priming is protected from Treg inhibition. Priming induces the expression of CXCR3 in a TCR affinity-dependent manner, which conditions the retention of activated T-cells in the priming region. Inability to express CXCR3 leads to T-cell relocation towards Treg-rich areas, where their expansion is limited by the lack of the costimulatory molecule CD70. Our study redefines the role of Treg during infection and provides a mechanism to explain how the priming and breadth of the CD8 T-cell response is protected during infection.

immunology↗

bioRxiv2024

Glycogen synthase kinase-3 is essential for Treg development and function

Tregs are critical regulators of the immune response, but the cellular signalling pathways that control their development and homeostasis remain to be determined. We found that glycogen synthase kinase-3 (GSK3), a kinase which integrates signals from AKT and mTOR, was essential for Treg development, restraining fatal autoimmunity. Loss of Gsk3 led to metabolic rewiring in Tregs, with disordered nucleotide metabolism and activation of OxPhos. Acute deletion of Gsk3 did not affect Treg frequency or numbers, but induced an effector gene expression program, and led to the formation of populations with pro-inflammatory signatures. The loss of Gsk3 in Tregs profoundly enhanced anti-tumoral immune responses and suppressed tumour growth.

immunology↗

bioRxiv2024

Autophagy acts as a brake on obesity-related fibrosis by controlling purine nucleoside signalling

A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Here, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features. We uncover that autophagy regulates purine nucleoside metabolism in obese adipocytes, preventing excessive release of the purine catabolites xanthine and hypoxanthine. Purines signal cell-extrinsically for fibrosis by driving macrophage polarisation towards a tissue reparative phenotype. Our findings reveal a novel role for adipocyte autophagy in regulating tissue purine nucleoside metabolism, thereby limiting obesity-associated fibrosis and maintaining the functional integrity of visceral WAT. Purine signals may serve as a critical balance checkpoint and therapeutic target in fibrotic diseases.

cell biology↗

bioRxiv2024

Cyclin-dependent kinase 5 (Cdk5) activity is modulated by light and gates rapid phase shifts of the circadian clock

The circadian clock enables organisms to synchronize biochemical and physiological processes over a 24-hour period. Natural changes in lighting conditions, as well as artificial disruptions like jet lag or shift work, can advance or delay the clock phase to align physiology with the environment. Within the suprachiasmatic nucleus (SCN) of the hypothalamus, circadian timekeeping and resetting rely on both membrane depolarization and intracellular second-messenger signaling. Voltage-gated calcium channels (VGCCs) facilitate calcium influx in both processes, activating intracellular signaling pathways that trigger Period (Per) gene expression. However, the precise mechanism by which these processes are concertedly gated remains unknown. Our study demonstrates that cyclin-dependent kinase 5 (Cdk5) activity is modulated by light and regulates phase shifts of the circadian clock. We observed that knocking down Cdk5 in the SCN of mice affects phase delays but not phase advances. This is linked to uncontrolled calcium influx into SCN neurons and an unregulated protein kinase A (PKA) - calcium/calmodulin-dependent kinase (CaMK) - cAMP response element-binding protein (CREB) signaling pathway. Consequently, genes such as Per1 are not induced by light in the SCN of Cdk5 knock-down mice. Our experiments identified Cdk5 as a crucial light-modulated kinase that influences rapid clock phase adaptation. This finding elucidates how light responsiveness and clock phase coordination adapt activity onset to seasonal changes, jet lag, and shift work.

neuroscience↗

bioRxiv2024

Inheritance of old mitochondria controls early CD8+ T cell fate commitment and is regulated by autophagy

T cell immunity is impaired during ageing, particularly in memory responses needed for efficient vaccination. Autophagy and asymmetric cell division (ACD) are cell biological mechanisms key to memory formation, which undergo a decline upon ageing. However, despite the fundamental importance of these processes in cellular function, the link between ACD and in vivo fate decisions has remained highly correlative in T cells and in the field of mammalian ACD overall. Here we provide robust causal evidence linking ACD to in vivo T cell fate decisions and our data are consistent with the concept that initiation of asymmetric T cell fates is regulated by autophagy. Analysing the proteome of first-daughter CD8+ T cells following TCR-triggered activation, we reveal that mitochondrial proteins rely on autophagy for their asymmetric inheritance and that damaged mitochondria are polarized upon first division. These results led us to evaluate whether mitochondria were asymmetrically inherited and to functionally address their impact on T cell fate. For this we used a novel mouse model that allows sequential tagging of mitochondria in mother and daughter cells, enabling their isolation and subsequent in vivo analysis of CD8+ T cell progenies based on pre-mitotic cell cargo. Autophagy-deficient CD8+ T cells showed impaired clearance and symmetric inheritance of old mitochondria, suggesting that degradation events promote asymmetry and are needed to generate T cells devoid of old organelles. Daughter cells inheriting old mitochondria are more glycolytic and upon adoptive transfer show reduced memory potential, whereas daughter cells that have not inherited old mitochondria from the mother cell are long-lived and expand upon cognate-antigen challenge. Proteomic and single-cell transcriptomic analysis of cells inheriting aged mitochondria suggest that their early fate divergence relies on one carbon metabolism as a consequence of poor mitochondrial quality and function. These findings increase our understanding of how T cell diversity is early-imprinted during division and will help foster the development of strategies to modulate T cell function. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/577412v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@526135org.highwire.dtl.DTLVardef@6c04b1org.highwire.dtl.DTLVardef@1a834fforg.highwire.dtl.DTLVardef@2f70f8_HPS_FORMAT_FIGEXP M_FIG The MitoSnap model allows tracking of pre-mitotic and post-mitotic cell cargoes. Both segregation and degradation (autophagy) contribute to the asymmetric inheritance of old mitochondria. Old mitochondria impact cell metabolism and function. Cells devoid of old mitochondria exhibit better memory potential in vivo. C_FIG

cell biology↗

bioRxiv2022

Asymmetric cell division safeguards memory CD8 T cell development

The strength of T cell receptor (TCR) stimulation and asymmetric distribution of fate determinants are both implied to affect T cell differentiation. Here, we uncovered asymmetric cell division (ACD) as a safeguard mechanism for memory CD8 T cell generation specifically upon strong TCR stimulation. Using live imaging approaches, we found that strong TCR stimulation induced elevated ACD rates and subsequent single cell derived colonies comprised both effector and memory precursor cells. The abundance of memory precursor cells emerging from a single activated T cell positively correlated with first mitosis ACD. Accordingly, preventing ACD by inhibition of PKC{zeta} during the first mitosis upon strong TCR stimulation markedly curtailed the formation of memory precursor cells. Conversely, no effect of ACD on fate commitment was observed upon weak TCR stimulation. Our data provide new mechanistic insights into the role of ACD for CD8 T cell fate regulation upon different activation conditions.

immunology↗

bioRxiv2021

Mapping of the autophagosomal degradome identifies IL-7Rα as key cargo in proliferating CD4+ T-cells

CD4+ T cells orchestrate both humoral and cytotoxic immune responses. While it is known that CD4+ T cell proliferation relies on autophagy, direct identification of the autophagosomal cargo involved is still missing. Here, we created a transgenic mouse model, which, for the first time, enables us to directly map the proteinaceous content of autophagosomes in any primary cell by LC3 proximity labelling. IL-7R, a cytokine receptor mostly found in naive and memory T cells, was reproducibly detected in autophagosomes of activated CD4+ T cells. Consistently, CD4+ T cells lacking autophagy showed increased IL-7R surface expression, while no defect in internalisation was observed. Mechanistically, excessive surface IL-7R sequestrates the common gamma chain, impairing the IL-2R assembly and downstream signalling crucial for T cell proliferation. This study provides proof-of-principle that key autophagy substrates can be reliably identified with this model to help mechanistically unravel autophagys contribution to healthy physiology and disease.

immunology↗

bioRxiv2021

Cell-extrinsic autophagy in mature adipocytes regulates anti-inflammatory response to intestinal tissue injury through lipid mobilization

Lipids play a major role in inflammatory diseases by altering inflammatory cell functions, through their use as energy substrates or as lipid mediators such as oxylipins. Autophagy, a lysosomal degradation pathway that limits inflammation, is known to impact on lipid availability, however whether this controls inflammation remains unexplored. We found that upon intestinal inflammation visceral adipocytes upregulate autophagy and that adipocyte-specific loss of the autophagy gene Atg7 exacerbates inflammation. While autophagy decreased lipolytic release of free fatty acids, loss of the major lipolytic enzyme Pnpla2/Atgl in adipocytes did not alter intestinal inflammation, ruling out free fatty acids as anti- inflammatory energy substrates. Instead, Atg7-deficient adipose tissues exhibited an altered oxylipin balance, driven through an NRF2-mediated upregulation of Ephx1. This was accompanied by a shift in adipose tissue macrophage polarization with reduced secretion of IL-10, leading to lower circulating levels of IL-10. These results suggest an underappreciated fat-gut crosstalk through an autophagy- dependent regulation of anti-inflammatory oxylipins, indicating a protective effect of adipose tissues for distant inflammation.

immunology↗

bioRxiv2021

Optical mini-stroke of thalamic networks impairs sleep stability, topography and cognition.

Modelling stroke in animals remains a challenge for translational research, especially for the infraction of small subcortical arteries. Using combined fibre optics and photothrombosis technologies, we developed a novel model of optically-induced infarcts (Opto-STROKE). Combining our model with electrophysiological recordings in freely-behaving mice, we studied early and late consequent patho-physiological changes in the dynamics of sleep-wake circuits and cognitive performance. Here, focusing on inducing Opto-STROKE lesions in the intralaminar thalamus (IL), which in humans cause severe impairments of arousal, cognition, and affective symptoms, our model recapitulated important deficits on sleep disorders presented in humans including arousal instability, concurrent to an augmented slow-wave activity and a reduction gamma power bands during wakefulness. Moreover, during NREM sleep, spindle density was decreased and topographically shifted to frontal cortices when compared to control animals. Remarkably, gamma power and spindle density were correlated with decreased pain threshold and impaired prefrontal cortex-dependent working memory in Opto-STROKE mice relative to controls. Collectively, our combined method influences both anatomical and functional outcomes of the classical stroke procedures and offers new insights on the fundamental role of the media thalamus as a hub for the regulation of both sleep-wake architecture and cognition. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗

bioRxiv2020

Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice

Neuroinflammation plays a crucial role during ageing and various neurological conditions, including Alzheimers disease, multiple sclerosis and infection. Technical limitations, however, have prevented an integrative analysis of how lymphocyte immune receptor repertoires and their accompanying transcriptional states change with age in the central nervous system (CNS). Here, we leveraged single-cell sequencing to simultaneously profile B cell receptor (BCR) and T cell receptor (TCR) repertoires and accompanying gene expression profiles in young and old mouse brains. We observed the presence of clonally expanded B and T cells in the central nervous system (CNS) of aged mice. Furthermore, many of these B cells were of the IgM and IgD isotype and had low levels of somatic hypermutation. Integrating gene expression information additionally revealed distinct transcriptional profiles of these clonally expanded lymphocytes. Our findings implicate that clonally related T and B cells in the CNS of elderly mice may contribute to neuroinflammation accompanying homeostatic ageing.

immunology↗

bioRxiv2020

Profiling virus-specific Tcf1+ T cell repertoires during acute and chronic viral infection

CD8 T cells play a crucial role in providing protection from viral infections. It has recently been established that a subset of CD8 T cells expressing Tcf1 are responsible for sustaining exhausted T cells during chronic lymphocytic choriomeningitis virus (LCMV) infection. Many of these studies, however, have been performed using T cell receptor (TCR) transgenic mice, in which CD8 T cells express a monoclonal TCR specific for the LCMV glycoprotein. To investigate whether the Tcf1+ and Tcf1-repertoires are naturally composed of similar or different clones in wild-type mice exposed to acute or chronic LCMV infection, we performed TCR repertoire sequencing of virus-specific CD8 T cells, including Tcf1+ and Tcf1-populations. Our analysis revealed that the Tcf1+ TCR repertoire is maintained at an equal or higher degree of clonal diversity despite harboring fewer cells. Additionally, within the same animal, there was extensive clonal overlap between the Tcf1+ and Tcf1-repertoires in both chronic and acute LCMV infection. We could further detect these virus-specific clones in longitudinal blood samples earlier in the infection. With respect to common repertoire parameters (clonal overlap, germline gene usage, and clonal expansion), we found minor differences between the virus-specific TCR repertoire of acute and chronic LCMV infection 40 days post infection. Overall, our results indicate that the Tcf1+ population emerging during chronic LCMV infection is not clonally distinct from the Tcf1-population, supporting the notion that the Tcf1+ pool is indeed a fuel for the more exhausted Tcf1-population within the heterogenous repertoire of LCMV-specific CD8 T cells.

immunology↗